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+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Biopieces(Package):
+ """The Biopieces are a collection of bioinformatics tools that can be
+ pieced together in a very easy and flexible manner to perform both
+ simple and complex tasks."""
+
+ homepage = "http://maasha.github.io/biopieces/"
+ git = "https://github.com/maasha/biopieces.git"
+
+ version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
+ submodules=True)
+
+ depends_on('perl', type=('build', 'run'))
+ depends_on('perl-module-build', type=('build', 'run'))
+ depends_on('perl-bit-vector', type=('build', 'run'))
+ depends_on('perl-svg', type=('build', 'run'))
+ depends_on('perl-term-readkey', type=('build', 'run'))
+ depends_on('perl-time-hires', type=('build', 'run'))
+ depends_on('perl-dbi', type=('build', 'run'))
+ depends_on('perl-xml-parser', type=('build', 'run'))
+ depends_on('perl-carp-clan', type=('build', 'run'))
+ depends_on('perl-class-inspector', type=('build', 'run'))
+ depends_on('perl-html-parser', type=('build', 'run'))
+ depends_on('perl-lwp', type=('build', 'run'))
+ depends_on('perl-soap-lite', type=('build', 'run'))
+ depends_on('perl-uri', type=('build', 'run'))
+ depends_on('perl-inline', type=('build', 'run'))
+ depends_on('perl-inline-c', type=('build', 'run'))
+ depends_on('perl-parse-recdescent', type=('build', 'run'))
+ depends_on('perl-version', type=('build', 'run'))
+ depends_on('perl-dbfile', type=('build', 'run'))
+ depends_on('perl-dbd-mysql', type=('build', 'run'))
+
+ depends_on('ruby@1.9:')
+ depends_on('ruby-gnuplot')
+ depends_on('ruby-narray')
+ depends_on('ruby-rubyinline')
+ depends_on('ruby-terminal-table')
+
+ depends_on('python@2.6:', type=('build', 'run'))
+ depends_on('blast-plus')
+ depends_on('muscle')
+ depends_on('mummer')
+ depends_on('blat')
+ depends_on('vmatch')
+ depends_on('bowtie')
+ depends_on('bwa')
+ depends_on('usearch')
+ depends_on('velvet')
+ depends_on('idba')
+ depends_on('ray')
+ depends_on('scan-for-matches')
+
+ def install(self, spec, prefix):
+ install_tree('.', prefix)
+
+ def setup_environment(self, spack_env, run_env):
+ # Note: user will need to set environment variables on their own,
+ # dependent on where they will want data to be located:
+ # BP_DATA - Contains genomic data etc.
+ # BP_TMP - Required temporary directory
+ # BP_LOG - Required log directory
+ run_env.prepend_path('BP_DIR', prefix)